Hughes confronted Ellison and other referees in the Hard Rock Stadium tunnel following Sunday's game in Miami and was seen on video shouting, "I'll catch you, trust me. I'll catch you guaranteed."
After the incident, the Bills defensive end denied the confrontation took place while speaking to reporters in the locker room and said he "would love to see the video" of him yelling.
"I lost the game so I'm supposed to angry," Hughes said, per The Buffalo News. "We just played our butts off for four quarters and we came six inches short of winning the game. I think myself and a lot of Buffalo Bills fans are upset right now. That's the nature of playing sports. Someone is going to win and someone is going to lose."
The league said the matter remains under review.
The NFL Referees Association released a statement regarding the incident.
"We fully expect the NFL's review to clear Roy Ellison," NFLRA executive director Scott Green said. "Video from last week's game shows he was verbally threatened by a player who has a well-documented history of abusive language and inappropriate actions towards our officials. While we are disappointed that the NFL has yet to address that aspect of the incident, we look forward to working with the League during its review and will ensure that Roy's rights are protected during this process."